Chapter 5. The Results Manager |
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This chapter explains how to use the Results Manager to view, save, and perform other functions on your program results. It also describes the different types of results and how you can interact with them, refine them for further analysis, and print them. About the Results ManagerThe Results Manager provides easy access to the analysis results generated by a program run. The results are organized by project, such that each time a member of a project runs an analysis, its results are automatically added to the Results Manager. Only those who are members of a project can access the project's results. Anyone who is a member of a project can add or delete results from a project or modify the description of analysis results.
Using the Results Manager, you can view and refine results for further analysis, and add or edit a description of the results. You can also save results as a text file, HTML file, or as a figure; and you can delete them. Unless you manually delete results, they are saved in the Results Manager indefinitely.
Note: If you do not see your most recent analysis results in the Results Manager, use your browser's reload command or the Refresh button to update the display.
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When you run a SeqWeb program, it generates a file that contains the analysis results, which can be viewed from either the Results Manager or the Job Manager. The format of the results is specific to the program that generated them. Results can include both text and graphics output. The text portion of the results can be saved either as hypertext markup language (HTML) or ASCII text; the graphics portion can be saved as a GIF or PNG file.
HTML
HTML is a format that is understood by web browsers. When you save results as HTML, you can reload them into a browser window at a later time for further study. Saving as HTML is especially useful when the results contain links to in-house databases or other databases on the Internet. Files saved as HTML are usable only within SeqWeb; they are not usable with SeqLab or the command-line Wisconsin Package.
Text
Files saved as text are usable within SeqWeb, SeqLab, and the command-line Wisconsin Package. If you do not plan to use SeqWeb results within SeqLab or the command-line Wisconsin Package, we recommend saving your results as HTML. Saving results in text format is useful when the results are a list file. (Although list files cannot be imported into SeqWeb, they are very useful in the command-line interface to the Wisconsin Package and in SeqLab, the X Windows-based graphical user interface to the Wisconsin Package.)
If the results contain multiple pages, SeqWeb saves them all to a single text file. If the results contain both text and graphics, SeqWeb saves only the text portion of the results in the text file.
Note: Before saving text files to your local computer, make sure the correct operating system file format is selected in the Preferences Manager.
Graphics
If the results include graphic output, you can save the graphic portion of the results as a GIF or PNG image. In certain cases, the graphics results display in a Viewer, which allows you to interact with the results to get additional information. From the Viewer, you can also save the graphic results as a figure for printing or including in other applications such as a word processor. See Interacting With the Viewers for more information about this capability.
SeqWeb uses color coding in the results and in the sequence displays to facilitate analysis. The base and residue characters within sequence alignments display in differentiating colors, which is useful for noting columns of aligned data that share the same color. PileUp, GrowTree, and ProfileSearch can display aligned sequences in color.
The designated colors for bases and residues are:
For DNA or RNA:
G = Black U or T = Green A = Red C = Blue
For Protein:
F (Phe) = Red B (Asp, Asn) = Dark Green Y (Tyr) = Red D (Asp) = Dark Green W (Trp) = Red E (Glu) = Dark Green H (His) = Light blue Z (Glu, Gln) = Dark Green N (Asn) = Light blue Q (Gln) = Green I (Ile) = Magenta K (Lys) = Blue V (Val) = Magenta R (Arg) = Blue L (Leu) = Magenta A (Ala) = Purple M (Met) = Magenta S (Ser) = Purple C (Cys) = Purple T (Thr) = Purple G (Gly) = Orange P (Pro) = Black
To view the results of an analysis from the Results Manager:
If you do not see the results that you want to view in the list, check the project name. If that is correct, use your browser's refresh or reload function to update the display.
The selected results display in a new browser window.
Note that if the program did not complete successfully, the Results Manager opens a window that contains a message to that effect.
Depending on the specific program that generated the results, you can then save or print the results. Some programs (such as Blast, FastA, FrameSearch, SSearch, Prime, CoilScan, HTHScan, and SPScan) generate graphic results in a separate viewer window that you can interact with to filter the display or to get additional detail. See Interacting With the Viewers for more information about this capability.
Refining Results
SeqWeb also provides an easy way to refine a program analysis to quickly regenerate the results. To refine the analysis that generated the results you are viewing, click on the Refine button on the results page. A window with the program that generated those results displays so that you can easily adjust the parameters and refine the analysis.
Some of the SeqWeb database search programs, such as Blast, FastA, FrameSearch, SSearch, Prime, CoilScan, HTHScan, and SPScan, display graphic results in a separate viewer window. In each case, the graphic view contains lines that represent a match or "hit" against the database. When you click on a line, a text view displays a description of the match below the graphic view. You can also interact with the viewer to filter the results that are displayed.
The Prime program also displays graphic results in a separate viewer. However, in this case, each line represents a product rather than a match, and there are different types of filters specific to this program's results.
The viewers provide easy access to some of the capabilities provided in the Sequence Editor, including the ability to annotate or view features. For example, you can zoom in and out of the display using the magnifying glass icons on the sides of the graphic display. When you move your mouse cursor over a line, you see more information about that item in the status line below the graphic display. When you click on a line, a text view displays with more detailed information about that item. From the viewers' text display, you can easily annotate a feature or select it for adding to your sequence list. Similar to elsewhere in SeqWeb, clicking on a sequence name displays the full text description and sequence string in a separate browser window.
You can also view the features associated with the query sequence by clicking on View Query Features in the View menu. A Feature Viewer window displays, showing the features associated with the sequence used in the analysis. From this window, you can annotate, save, or delete features just as you can elsewhere in SeqWeb.
In addition, the viewers also allow you to search the results for a specific match, or search the definition line for a specific string. You can also save the graphic display as a figure for including in another application. The capabilities similar to those described elsewhere in this document are not repeated here. Only those functions unique to the viewers are described in this section.
Filtering Database Search Results
The graphic results from database searching programs such as BLAST, FastA, FrameSearch, and SSearch viewers can be filtered using the results viewer. The viewers provide two ways to filter the display of their results, by Hit Score or by Rank, as follows:
To change the Hit Score Filter, select or de-select the check boxes at the top of the display.
To change the Rank Filter, use the arrows or type in a new number between 1 and 250. Note that the E-value changes accordingly.
The BLAST, FastA, FrameSearch, and SSearch viewers also provide a way to search the definition line for a text string.
To search for a string:
You can also go to a specific hit by typing that number preceded by the # sign (for example, #100 for the 100th hit).
If no match is found, a message to that effect appears in the status line.
If a match is found, that sequence line is highlighted in the graphic view, and the description appears in the text view.
If no match is found upon subsequent searches, a message to that effect appears in the status line.
Clicking on Reset clears the search string contents and repositions the search start at the first line.
From the viewers, you can also save the graphic results as a figure for printing or including in another application, such as a word processor. However, in this case, only the graphics portion of the output is saved.
To save graphic results as a figure:
(Remember, this capability is not available for every program.)
A new browser window displays containing the graphic as a GIF or PNG file.
The GIF or PNG file is saved on the server. You can also save the image to your local computer using your browser's Save Image As (Netscape) or Save Picture (Internet Explorer) capability.
You can print SeqWeb analysis results using your browser's print capability.
To print the contents of a results window:
The results file opens in a new browser window.
Note: To print graphics output from programs that generate results in a viewer, you must first save the results as a figure, then use your browser to print that output.
With the Results Manager, you can edit the description associated with a results file to make it more meaningful to you. The description appears in the status bar at the bottom of the Results Manager window when you select a results filename.
To edit a results file description:
The Edit window displays with the current description.
Clicking the Clear button will quickly delete the entire description.
Clicking the Reset button after editing will bring back the previous description.
SeqWeb lets you save program results to your local computer from within the Results Manager, or any time that you are viewing results. You can save the text portion of the results as either HTML or text. If the results contain both text and graphics, SeqWeb saves only the text portion of the results in the text file. See Saving a Figure for more information about saving graphics output.
Warning: If your SeqWeb output has multiple files associated with it, be cautious about renaming the files as you save them to your local computer. Output that has multiple files contains links within each file to the other files associated with it. Therefore, renaming any of the files would break the links between them.
To save text results to your local computer:
Note: If you do not see the results that you want to save in the list, check the project name. If that is correct, use your browser's refresh or reload function to update the display.
An Unknown File Type dialog box appears.
A Save As... dialog box appears.
SeqWeb displays a Save As... dialog box for each file you selected. Note that some analysis results have graphics or multiple pages associated with them. For example, if you ran the BLAST program, you might see results that are lengthy. For ease of use, SeqWeb breaks these results into multiple pages. Consequently, when you save BLAST results, SeqWeb displays a Save As dialog box for each page of those results. A Save As dialog box also appears separately for each graphic image.
A Save As... window appears, displaying all the files associated with the single results filename you chose. These associated files may be graphics or may be the result of a lengthy output file that SeqWeb has split into multiple files for ease of use.
A File Download dialog box appears.
A Save As... dialog box appears.
The results are saved to the specified directory on your local computer, with the specified filename(s).
Any member of a SeqWeb project can delete the results associated with a project from the server. The SeqWeb files you may have saved to your local computer are not affected.
To delete results from the server:
SeqWeb deletes the selected file(s) from the server, and updates the results list accordingly. Your local computer files are not affected.
